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- PDB-7y2x: Ni-Carbonic Anhydrase II complexed with 3NPA after UV at 200 K -

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Basic information

Entry
Database: PDB / ID: 7y2x
TitleNi-Carbonic Anhydrase II complexed with 3NPA after UV at 200 K
ComponentsCarbonic anhydrase 2
KeywordsMETAL BINDING PROTEIN / carbonic anhydrase / enzyme mechanism / metalloenzymes
Function / homology
Function and homology information


positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway ...positive regulation of cellular pH reduction / positive regulation of dipeptide transmembrane transport / regulation of monoatomic anion transport / secretion / cyanamide hydratase / cyanamide hydratase activity / arylesterase activity / regulation of chloride transport / Reversible hydration of carbon dioxide / angiotensin-activated signaling pathway / positive regulation of synaptic transmission, GABAergic / morphogenesis of an epithelium / regulation of intracellular pH / carbonic anhydrase / carbonate dehydratase activity / carbon dioxide transport / Erythrocytes take up oxygen and release carbon dioxide / Erythrocytes take up carbon dioxide and release oxygen / neuron cellular homeostasis / one-carbon metabolic process / apical part of cell / myelin sheath / extracellular exosome / zinc ion binding / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Carbonic anhydrase, alpha-class, conserved site / Alpha-carbonic anhydrases signature. / Carbonic anhydrase, alpha-class / Alpha carbonic anhydrase domain / Alpha carbonic anhydrase domain superfamily / Eukaryotic-type carbonic anhydrase / Alpha-carbonic anhydrases profile. / Eukaryotic-type carbonic anhydrase
Similarity search - Domain/homology
2-(3-NITROPHENYL)ACETIC ACID / NICKEL (II) ION / Carbonic anhydrase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsKim, C.U. / Kim, J.K.
Funding support Korea, Republic Of, 1items
OrganizationGrant numberCountry
Other privateSSTF-BA1702-04 (Samsung Science and Technology Foundation) Korea, Republic Of
CitationJournal: To Be Published
Title: Temperature series of human Carbonic Anhydrase II with photolysis of caged CO2
Authors: Kim, C.U. / Kim, J.K.
History
DepositionJun 9, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 20, 2023Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Carbonic anhydrase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,5884
Polymers29,2891
Non-polymers2993
Water4,360242
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-18 kcal/mol
Surface area11760 Å2
MethodPISA
Unit cell
Length a, b, c (Å)42.490, 41.324, 71.965
Angle α, β, γ (deg.)90.00, 104.04, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Carbonic anhydrase 2 / / Carbonate dehydratase II / Carbonic anhydrase C / CAC / Carbonic anhydrase II / CA-II


Mass: 29289.062 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CA2 / Production host: Escherichia coli (E. coli) / References: UniProt: P00918, carbonic anhydrase
#2: Chemical ChemComp-NI / NICKEL (II) ION / Nickel


Mass: 58.693 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Ni / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MNP / 2-(3-NITROPHENYL)ACETIC ACID


Mass: 181.145 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H7NO4 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 242 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.09 Å3/Da / Density % sol: 41.22 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.8 / Details: 1.3 M sodium citrate, 50 mM Tris-HCl

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Data collection

DiffractionMean temperature: 200 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å
DetectorType: ADSC QUANTUM 270 / Detector: CCD / Date: Dec 2, 2020
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97934 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. obs: 37959 / % possible obs: 97 % / Redundancy: 3.8 % / CC1/2: 0.995 / CC star: 0.999 / Rmerge(I) obs: 0.06 / Rpim(I) all: 0.037 / Rrim(I) all: 0.071 / Net I/σ(I): 20.6
Reflection shellResolution: 1.5→1.53 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.438 / Mean I/σ(I) obs: 4.1 / Num. unique obs: 1854 / CC1/2: 0.829 / CC star: 0.952 / Rpim(I) all: 0.259 / Rrim(I) all: 0.509 / % possible all: 94.6

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
HKL-2000data reduction
HKL-2000data scaling
REFMAC5.8.0135phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6LV5

6lv5


Resolution: 1.5→29.18 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.968 / SU B: 2.269 / SU ML: 0.038 / Cross valid method: FREE R-VALUE / ESU R: 0.07 / ESU R Free: 0.063 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.15796 1929 5.1 %RANDOM
Rwork0.1107 ---
obs0.11316 35950 96.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.333 Å2
Baniso -1Baniso -2Baniso -3
1--0.02 Å2-0 Å20 Å2
2--0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.5→29.18 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2049 0 15 242 2306
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0290.0192253
X-RAY DIFFRACTIONr_bond_other_d0.0020.022079
X-RAY DIFFRACTIONr_angle_refined_deg2.4681.9533075
X-RAY DIFFRACTIONr_angle_other_deg1.24834835
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.635287
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.70725.047107
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.30615375
X-RAY DIFFRACTIONr_dihedral_angle_4_deg24.503157
X-RAY DIFFRACTIONr_chiral_restr0.1850.2319
X-RAY DIFFRACTIONr_gen_planes_refined0.0130.0212610
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02521
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it3.2161.6921088
X-RAY DIFFRACTIONr_mcbond_other3.0231.6871087
X-RAY DIFFRACTIONr_mcangle_it3.4052.5561377
X-RAY DIFFRACTIONr_mcangle_other3.4032.561378
X-RAY DIFFRACTIONr_scbond_it4.9712.1331165
X-RAY DIFFRACTIONr_scbond_other4.932.131164
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.7383.0131689
X-RAY DIFFRACTIONr_long_range_B_refined6.9915.6372676
X-RAY DIFFRACTIONr_long_range_B_other6.98915.6412677
X-RAY DIFFRACTIONr_rigid_bond_restr4.98234332
X-RAY DIFFRACTIONr_sphericity_free55.299570
X-RAY DIFFRACTIONr_sphericity_bonded14.95954424
LS refinement shellResolution: 1.5→1.539 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.211 152 -
Rwork0.136 2573 -
obs--95.05 %

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